[Transposonpsi-users] transposonpsi and getting psiblast to work.

[Brian H. <bh...@br...>]

Hi Anna,

If you don't have one already, you may need to set up a ~/.ncbirc file
that indicates the path to the blast-installed data directory, where
the blosum matrix exists.

Some info on the .ncbirc file is here:
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html

My file looks like so:

[NCBI]
DATA=/seq/annotation/bio_tools/NCBI_BLAST/blast-2.2.17/data


Best,

-brian




-----------------
Hello, I am having this problem when trying to run transposonPSI.pl
with my proteins fasta file:

perl transposonPSI.pl
/Volumes/disk3/AnnaE/programs/cufflinks-0.9.0.OSX_x86_64/24GONA_novo/common_u_NO_artifacts-genes-longest-f100-prot-exactlyone-aug-prot.fasta
prot

processing CUFF.1333761.1.
    blast against
/Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq
CMD: blastpgp -i
/Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq
-d transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.seq
-R /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.chk
-j 1 -e 1e-5 > transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.cacta.refSeq.psitblastn
[blastpgp 2.2.24] WARNING: -t larger than 1 not supported when
restarting from a checkpoint; setting -t to 1

[blastpgp 2.2.24] WARNING: Unable to open BLOSUM62
[blastpgp 2.2.24] WARNING: BlastScoreBlkMatFill returned non-zero status
[blastpgp 2.2.24] WARNING: SetUpBlastSearch failed.
sh: line 1: 72000 Bus error              blastpgp -i
/Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq
-d transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.seq
-R /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.chk
-j 1 -e 1e-5 > transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.cacta.refSeq.psitblastn
Error blastpgp -i
/Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq
-d transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.seq
-R /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.chk
-j 1 -e 1e-5 > transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.cacta.refSeq.psitblastn
35328 at transposonPSI.pl line 142, <$filehandle> line 1.

Any idea about how to solve this?
Thanks a lot!

Anna Esteve Codina
Departament de Ciència Animal i dels Aliments
Facultat de Veterinària
Universitat Autònoma de Barcelona
telf:93 5814260




-- 
--
Brian J. Haas
Manager, Bioinformatics Outreach, Genome Annotation and Analysis
The Broad Institute
http://broad.mit.edu/~bhaas